Biology subjects

Athanasiadis, A.

Publications and source records attributed to Athanasiadis, A..

9 recordsLinked to original sources

bioRxiv2026

A novel proviral mechanism for the ISG, Shiftless, during human coronavirus infection

As highly pathogenic human coronaviruses continue to emerge from zoonotic sources, understanding how host intrinsic immune responses control infection is critical for preventing severe disease. The interferon (IFN) pathway induces antiviral effectors, including the interferon-stimulated gene (ISG) Shiftless (SHFL), which restricts -1 programmed ribosomal frameshifting during SARS-CoV-2 infection. Here, we investigate a novel proviral mechanism for SHFL using loss-of-function and gain-of-function approaches. Despite its established antiviral activity, SHFL enhanced infection by SARS-CoV-2 and the seasonal coronavirus HCoV-229E by increasing cellular susceptibility to infection. SHFL further promoted coronavirus infection by reducing cellular sensitivity to IFN, potentially through modulation of JAK/STAT signaling. Finally, we demonstrate that SHFL-mediated enhancement of baseline viral susceptibility is partially dependent on the domain previously implicated in its antiviral inhibition of -1 programmed ribosomal frameshifting. In contrast, SHFL-mediated regulation of IFN signaling is independent of this domain. Together, these findings establish SHFL as a dual-function ISG with distinct proviral and antiviral activities, highlighting the complex roles of innate immune effectors during coronavirus infection.

microbiology↗

bioRxiv2026

Genetic accessibility, not superior fitness, determines which anti-HBs antibody escape variants are selected in patients

Background and Aims: Genetic diversity within the hepatitis B virus (HBV) surface antigen (HBsAg) drives the emergence of immune escape variants, but studying this diversity in vivo has been limited by the difficulty of establishing infection from patient isolates. We aimed to perform unbiased in vivo screening of variants in the HBs antigenic loop for antibody escape and fitness, using synthetic DNA launch of HBV in human hepatocyte chimeric mice. Approach and Results: Direct intrahepatic injection (IHI) of barcoded, recombinant cccDNA established infection from up to 32,000 independent launch events of a genotype A strain and successfully launched clinical consensus sequences across the major genotypes. Using IHI, we performed deep mutational scanning of 4,608 codon variants across the HBs antigenic loop. Under control antibody treatment, diverse variants expanded, revealing differences in variant fitness in the absence of adaptive immune pressure. Anti-HBs monoclonal antibody treatment suppressed wild-type viremia while permitting breakthrough of resistant variants from the library. Sequencing identified strong enrichment for substitutions at G145 (G145Q, G145H, G145R). Notably, G145Q, rather than the clinically dominant G145R, showed the greatest fitness advantage, indicating that G145R's clinical prevalence does not reflect superior intrinsic fitness. Conclusions: Unbiased in vivo screening reveals that clinically observed HBV escape mutations reflect which substitutions are genetically accessible by single nucleotide change and compatible with the overlapping polymerase reading frame, rather than which confer optimal fitness. This approach establishes a platform for high-resolution mapping of viral variant fitness under antiviral selection pressure.

microbiology↗

bioRxiv2026

The HBV basal core promoter mutation confers a replicative advantage and transcriptionally reprograms hepatocytes toward HCC subtypes

Background: Hepatitis B virus (HBV) basal core promoter (BCP) and precore (PC) mutations occur during chronic HBV infection with the BCP-mutant being associated with increased hepatocellular carcinoma (HCC) risk. Objectives: The effects of these mutants on viral replication, hepatocyte biology, and carcinogenesis remain poorly defined. To address this, we characterized BCP- and PC-mutants using human hepatocyte chimeric mice and asked whether the resulting infection-induced transcriptomes correspond to subsets of human HBV-related hepatocellular carcinomas (HBV-HCCs). Design: Isogenic wild-type (WT), BCP- and PC-mutants of HBV genotypes A, C, and D (HBV-A, -C, -D) were generated from recombinant covalently-closed circular DNA to infect chimeric mice. HBV-HCC transcriptomic datasets from The Cancer Genome Atlas (TCGA) were used to stratify association of HBV variants with HCC subtypes. Results: WT, BCP-mutant, and PC-mutant HBV sequences remained genetically stable. The BCP mutation, but not the PC mutation, accelerated the rise in serum viremia in HBV-D- and HBV-A-infected chimeras; in HBV-C, acceleration required both (PC+BCP) mutations. Further comparisons of HBV-D variants revealed that the BCP-mutant increased intrahepatic viral DNA, viral protein expression, and upregulated cancer-related pathways, including transcripts associated with a subset of HBV-HCCs. Analysis of HBV-HCC samples from the TCGA revealed that tumors often harbor a mixture of WT and mutant transcripts, and that WT- and BCP-mutant-associated HCCs exhibit distinct transcriptional profiles. Conclusions: The HBV BCP-mutant directly perturbs hepatocyte homeostasis via virus-intrinsic mechanisms, selectively activating cancer-related pathways and defining a molecularly distinct subset of HBV-HCC. These findings suggest that HBV variants form distinct subcategories of HBV-HCCs.

molecular biology↗

bioRxiv2026

A CRISPR-Cas9 platform for primary human hepatocytes enables arrayed screening and in vivo validation of HBV host factors

More than two million deaths annually are attributed to liver-related conditions, making primary human hepatocytes (PHH) an invaluable in vitro model for studying liver pathophysiology and the molecular mechanisms underlying hepatic diseases. However, because PHH do not proliferate in culture, CRISPR gene editing has been highly inefficient. Here, we report lipofection- and lentivirus-mediated protocols for CRISPR-Cas9 delivery in mouse-passaged primary human hepatocytes (mpPHH), a system that enables PHH expansion in liver-humanized mice. We achieve robust gene editing efficiencies exceeding 90% in mpPHH while maintaining cell viability. We demonstrate the utility of these protocols by disrupting CYP3A4 to impair xenobiotic metabolism and by showing that edited mpPHH efficiently engraft and expand in mice, generating liver-humanized animals. We establish the feasibility of arrayed CRISPR screening in mpPHH using an 85-gene screen to identify host factors influencing hepatitis B virus (HBV) infection, and validate key findings in humanized mice by targeting the HBV entry receptor SLC10A1 (NTCP), which reduced viral infection in vivo. Our methodology enables scalable genetic manipulation of mpPHH, opening new avenues for HBV research and liver disease modeling.

genomics↗

bioRxiv2026

Orthogonal CRISPR screens and human liver chimeric mice identify hepatitis B virus host factors

Hepatitis B virus (HBV) chronically infects approximately 250 million people worldwide, and reliable curative therapies are lacking. A broader understanding of viral-host interactions could accelerate efforts to find new host-centric therapeutic targets. However, inefficient cell culture systems and limited replication markers compatible with pooled screening have precluded the widespread use of genetic perturbation screens. Here, we performed the first pooled, genome-wide CRISPR-Cas9 knockout (KO) screen with authentic HBV infection and integrated these results with two orthogonal pooled screens to identify host factors. We selected 72 genes for a multi-step assessment that included arrayed validation assays using both HBV infection and pgRNA transfection. We then independently tested thirteen genes using high-efficiency bulk KO experiments to guide further investigations of both antiviral and proviral factors. In both KO and siRNA-mediated knockdown experiments, depletion of the top antiviral factor, EXOC1, enhanced multiple HBV replication markers, and transcriptomic analysis revealed activation of hypoxia- and HIF-1 gene signatures. Three proviral factors, IRF2, WDR48, and ZCCHC14, were investigated in vivo using a human liver chimeric mouse model, which demonstrated that ZCCHC14 KO greatly reduced HBV replication and spread. Together, these complementary in vitro and in vivo platforms expand the catalog of HBV host factors and provide a scalable framework for host target discovery.

microbiology↗

bioRxiv2026

Effects of lovastatin on auxin transport and root development in Arabidopsis thaliana

Sterol biosynthesis underlies significant physiological functions in plants, including the production of membrane structural sterols and hormones such as brassinosteroids and cytokinins. Inhibition of sterol biosynthesis has been shown to disrupt multiple aspects of Arabidopsis thaliana development. Here, the effects of lovastatin, an inhibitor of HMG-CoA reductase, on root development were investigated, focusing on auxin-cytokinin distribution and transport. Lovastatin inhibited primary root growth, especially cell elongation, in a dose-dependent manner. Additionally, lateral root density was considerably increased and lateral root primordia (LRP) emerged ectopically. In accordance to the above defects, auxin/cytokinin imbalance was recorded by the ectopic presence of the synthetic auxin marker DR5 and a significant decrease of cytokinins, as revealed by depletion of the TCS (two-component signaling) marker. Because auxin distribution appeared disturbed, auxin transport impairment was further examined. Plasma membrane localization of PIN auxin efflux carriers declined significantly, showing additional diffuse cytoplasmic localization in LRP cells. However, the cell-specific localization patterns of several PINs and their abundance at the transcript and protein level appeared unaffected or slightly increased. Fluorescence recovery after photobleaching (FRAP) analysis regarding membrane kinetics of PIN2 revealed altered PIN2 membrane dynamics and transmission electron microscopy (TEM) observations showed structural defects at the plasma membrane-cell wall interface. Together, these results support that sterol biosynthesis is essential for maintaining plasma membrane organization, which, in turn, is key factor for the distribution of hormones that control root development. HighlightsLovastatin treatment inhibits root growth and causes deregulated formation of lateral roots. Consistently, lovastatin causes altered patterns of auxin distribution relevant to PIN protein mis-localization and decreases cytokinin levels. These changes could be attributed to reduced structural sterols as exemplified from alteration in PIN2 membrane dynamics.

plant biology↗

bioRxiv2024

Principles and Operation of Virtual Brain Twins

Current clinical methods often overlook individual variability by relying on population-wide trials, while mechanism-based trials remain underutilized in neuroscience due to the brains complexity. A Virtual Brain Twin (VBT) is a personalized digital replica of an individuals brain, integrating structural and functional brain data into advanced computational models and inference algorithms. By bridging the gap between molecular mechanisms, whole-brain dynamics, and imaging data, VBTs enhance the understanding of (patho)physiological mechanisms, advancing insights into both healthy and disordered brain function. Central to VBT is the network modeling that couples mesoscopic representation of neuronal activity through white matter connectivity, enabling the simulation of brain dynamics at a network level. This transformative approach provides interpretable predictive capabilities, supporting clinicians in personalizing treatments and optimizing interventions. This manuscript outlines the key components of VBT development, covering the conceptual, mathematical, technical, and clinical aspects. We describe the stages of VBT construction-from anatomical coupling and modeling to simulation and Bayesian inference-and demonstrate their applications in resting-state, healthy aging, epilepsy, and multiple sclerosis. Finally, we discuss potential extensions to other neurological disorders, such as Parkinsons disease, and explore future applications in consciousness research and brain-computer interfaces, paving the way for advancements in personalized medicine and brain-machine integration. "The brain is conceived as a self-organizing system operating close to instabilities where its activities are governed by collective variables, the order parameters, that enslave the individual parts, i.e., the neurons." Professor Hermann Haken (1927-2024).

neuroscience↗

bioRxiv2022

Thermodynamic analysis of Zα domain-nucleic acid interactions

DNA/RNA molecules adopting the left-handed conformation (Z-form) have been attributed with immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Z domains) in varied proteins that are involved in the innate immune response, such as the interferon inducible form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the poxvirus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Z domain-containing proteins recognise left-handed Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in virus recognition. Given these important emerging roles for the Z domains, it is pivotal to understand the mechanism of recognition of the Z-DNA/Z-RNA by these domains. To this end, we assessed the binding thermodynamics of Z domain from ORF112 and ADAR1 on T(CG)3 and T(CG)6 oligonucleotides which have high propensity to adopt the Z-conformation. Our study highlights important differences in the mode of binding by the two Z domains originating from different proteins. Site-directed mutagenesis was employed together with isothermal titration calorimetry to tease apart finer details of the binding thermodynamics. Our work advances the understanding on binding thermodynamics of Z domains to their cognate nucleic acid substrates and contributes to the efforts to gain a complete appreciation of this process.

biochemistry↗

bioRxiv2021

Enrichment of Zα domains at cytoplasmic stress granules is due to their innate ability to bind nucleic acids

Z domains are a subfamily of winged Helix-Turn-Helix (wHTH) domains found exclusively in proteins involved in the nucleic acids sensory pathway of vertebrate innate immune system and host evasion by viral pathogens. Interestingly, they are the only known protein domains that recognise the left-handed helical conformation of both dsDNA and dsRNA, known as Z-DNA and Z-RNA. Previously, it has been demonstrated that ADAR1 and ZBP1, two proteins possessing the Z domains, localize to cytosolic stress granules. It was further speculated that such localization is principally mediated by Z domains. To characterize and better understand such distinct and specific localization, we characterised the in vivo interactions and localization pattern for the amino terminal region of human DAI harbouring two Z domains (Z{beta}DAI). Using immunoprecipitation and mass spectrometry, we identified several interacting partners that were components of the complex formed by Z domains and RNAs. Differential interacting partners to wild-type Z, relative to mutant proteins, demonstrated that most of the physiologically relevant interactions are mediated by the nucleic acid binding ability of the Z{beta}. Further, we also show enrichment of selected complex components in cytoplasmic stress granules under conditions of stress. This ability is mostly lost in the mutants of Z{beta}DAI (Z{beta}DAI 4xmut) that lack nucleic-acid binding ability. Thus, we posit that the mechanism for the translocation of Z domain-containing proteins to stress granules is mainly mediated by the nucleic acid binding ability of their Z domains. Finally, we demonstrate that FUS and PSF/p54nrb, two RNA binding proteins with established roles in stress granules, interact with Z, which provides strong evidence for a role of these proteins in the innate immune system.

biochemistry↗